In many parts of the Global South, food systems are confronted with complex sustainability challenges including high levels of poverty, food insecurity, malnutrition, disempowerment, and degraded environments. Transformation is broadly discussed in research, policy, and planning as the systemic change required to address complex sustainability issues. Transformation of food systems has become a global priority for research and action. However, transformation processes are not neutral, but are associated with losses and gains that are unevenly distributed. Institutions play an important role in relation to how transformation of food systems occur and with what outcomes. Empirical understandings of how institutions can influence transformation processes in a way that avoids risks or the so-called dark side of transformation are needed. This article aims to contribute towards understanding the roles that institutions play in transformation processes in the context of Global South food systems through synthesising insights from transdisciplinary case studies. The three case studies include multi-purpose cooperative institutions in farming areas in southwest Ethiopia, fisherfolk organisations in aquatic food-producing areas in northern Philippines, and Gotong Royong for irrigation canal management for pond aquaculture in Indonesia. The article examines whether and how institutions advance inclusion and participation in food systems, and whether institutions enable or constrain food system actors in mitigating or avoiding transformation risks. The paper reflects on the role of community-level institutions and hybrid governance arrangements, and the interplay of structure and agency in transformation processes.